BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778915.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 36,584,512 number of mapped reads = 35,370,280 (96.68%) number of supplementary alignments = 245,973 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,901,566 number of mapped paired reads (second in pair) = 17,468,714 number of mapped paired reads (both in pair) = 34,804,738 number of mapped paired reads (singletons) = 565,542 number of mapped bases = 3,530,808,522 bp number of sequenced bases = 3,529,908,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,030,691 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 64,886.1405 std insert size = 2,445,639.6515 median insert size = 278 >>>>>>> Mapping quality mean mapping quality = 53.7217 >>>>>>> ACTG content number of A's = 1,059,019,740 bp (30%) number of C's = 700,463,933 bp (19.84%) number of T's = 1,054,977,065 bp (29.89%) number of G's = 714,282,969 bp (20.24%) number of N's = 1,164,925 bp (0.03%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 19,836,325 number of insertions = 350,000 mapped reads with insertion percentage = 0.98% number of deletions = 406,715 mapped reads with deletion percentage = 1.13% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 1.1406X std coverageData = 4.6659X There is a 46.69% of reference with a coverageData >= 1X There is a 26.72% of reference with a coverageData >= 2X There is a 15.53% of reference with a coverageData >= 3X There is a 9.15% of reference with a coverageData >= 4X There is a 5.45% of reference with a coverageData >= 5X There is a 3.3% of reference with a coverageData >= 6X There is a 2.02% of reference with a coverageData >= 7X There is a 1.26% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 248321951 0.9962741517101376 11.711604620905563 chr2 243199373 271648037 1.1169767160542803 2.612400615011128 chr3 198022430 289349023 1.4611931739247923 1.9721312381249552 chr4 191154276 195367386 1.022040364924926 1.8853794478679196 chr5 180915260 165735425 0.9160942255506804 1.5248303562396799 chr6 171115067 241555969 1.41165809203698 2.6527281585349853 chr7 159138663 267222624 1.6791810296910687 4.749900162204037 chr8 146364022 328722445 2.245923830926155 2.681402266653296 chr9 141213431 145103886 1.027550176866675 3.552936481187756 chr10 135534747 88646971 0.6540534657138513 9.94816016447255 chr11 135006516 139315440 1.031916415056589 1.828769463006364 chr12 133851895 138384874 1.033865631861245 1.8010259078699522 chr13 115169878 118542506 1.0292839417612303 1.7314137828456673 chr14 107349540 114234617 1.0641369958362188 1.780586583269991 chr15 102531392 120487663 1.1751294959498844 1.9751016903469916 chr16 90354753 96394723 1.0668472858312168 1.8983671335850203 chr17 81195210 62071953 0.7644780153903168 4.039019691281232 chr18 78077248 113042648 1.4478308456773477 3.7352881576288546 chr19 59128983 64835370 1.0965074437353337 6.468229774314763 chr20 63025520 90293923 1.4326565334169397 2.2033890229504443 chr21 48129895 38219319 0.794086897550888 1.603351495480342 chr22 51304566 25479023 0.4966229126662917 1.2388266967894288 chrMT 16571 3149 0.19003077665801701 0.619261819582539 chrX 155270560 165283209 1.064485173493288 1.764440109229341 chrY 59373566 2546388 0.04288757053938785 0.5670999059359374